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Coexpression cluster:C1813: Difference between revisions

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|full_id=C1813_somatostatinoma_melanoma_mesenchymal_placenta_smallcell_Keratocytes_renal
|full_id=C1813_somatostatinoma_melanoma_mesenchymal_placenta_smallcell_Keratocytes_renal
|id=C1813
|id=C1813
|ontology_enrichment_celltype=CL:0000066!5.69e-28!254;CL:0000220!1.35e-23!246;CL:0002321!1.51e-23!248;CL:0000222!2.28e-19!119;CL:0000548!1.21e-13!679;CL:0000004!1.21e-13!679;CL:0000255!1.21e-13!679;CL:0000012!9.61e-13!682;CL:0000055!1.21e-12!180;CL:0002139!1.60e-11!24;CL:0002078!5.53e-11!44;CL:0000213!5.54e-11!57;CL:0000215!5.54e-11!57;CL:0000115!1.61e-10!35;CL:0000183!1.46e-09!59;CL:0000192!3.08e-09!42;CL:0000514!3.08e-09!42;CL:0000071!1.12e-08!18;CL:0002546!1.12e-08!18;CL:0000187!4.08e-08!54;CL:0000680!5.15e-08!57;CL:0000056!5.15e-08!57;CL:0000355!5.15e-08!57;CL:1000497!2.01e-07!18;CL:0002518!2.01e-07!18;CL:0000144!3.09e-07!625;CL:0000076!5.17e-07!62;CL:0000393!7.17e-07!60;CL:0000211!7.17e-07!60
|ontology_enrichment_celltype=CL:0000066!1.73e-10!253;CL:0002321!1.08e-08!250;CL:0002139!1.16e-08!24;CL:0000147!1.01e-07!14;CL:0000222!1.76e-07!121;CL:0000071!9.09e-07!18;CL:0002546!9.09e-07!18
|ontology_enrichment_disease=DOID:305!3.63e-07!106
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002100!2.76e-19!216;UBERON:0003914!4.23e-18!118;UBERON:0002049!1.89e-16!79;UBERON:0007798!1.89e-16!79;UBERON:0000055!5.48e-15!69;UBERON:0000490!1.32e-14!138;UBERON:0003104!1.70e-14!238;UBERON:0009142!1.70e-14!238;UBERON:0000466!1.74e-14!126;UBERON:0009569!1.59e-13!113;UBERON:0004872!1.42e-12!84;UBERON:0001981!2.24e-12!60;UBERON:0007500!2.24e-12!60;UBERON:0004537!2.24e-12!60;UBERON:0006965!2.24e-12!60;UBERON:0000464!2.40e-12!104;UBERON:0003886!6.08e-12!63;UBERON:0005256!1.80e-11!143;UBERON:0002553!1.24e-10!70;UBERON:0000468!1.94e-10!659;UBERON:0005177!2.42e-10!107;UBERON:0001637!2.91e-10!42;UBERON:0003509!2.91e-10!42;UBERON:0004572!2.91e-10!42;UBERON:0000926!7.59e-10!448;UBERON:0004120!7.59e-10!448;UBERON:0006603!7.59e-10!448;UBERON:0006554!1.45e-09!44;UBERON:0001008!2.69e-09!45;UBERON:0002417!9.95e-09!61;UBERON:0000916!9.95e-09!61;UBERON:0001986!1.12e-08!18;UBERON:0004638!1.12e-08!18;UBERON:0004852!1.12e-08!18;UBERON:0000487!1.21e-08!22;UBERON:0004573!1.61e-08!33;UBERON:0004571!1.61e-08!33;UBERON:0004535!2.51e-08!110;UBERON:0006914!5.30e-08!25;UBERON:0001009!5.53e-08!113;UBERON:0000119!7.98e-08!312;UBERON:0001048!8.46e-08!168;UBERON:0003064!1.06e-07!37;UBERON:0005172!1.19e-07!55;UBERON:0005173!1.19e-07!55;UBERON:0004119!1.22e-07!169;UBERON:0000925!1.22e-07!169;UBERON:0006595!1.22e-07!169;UBERON:0002323!1.29e-07!46;UBERON:0000481!1.48e-07!347;UBERON:0000483!1.55e-07!309;UBERON:0005156!1.98e-07!59;UBERON:0000990!1.98e-07!59;UBERON:0004458!2.16e-07!49;UBERON:0004921!2.77e-07!129;UBERON:0004185!2.77e-07!129;UBERON:0000947!3.50e-07!21;UBERON:0010191!3.50e-07!21;UBERON:0001134!4.00e-07!61;UBERON:0002036!4.00e-07!61;UBERON:0003082!4.00e-07!61;UBERON:0004111!6.46e-07!241;UBERON:0000467!7.57e-07!625;UBERON:0002385!7.80e-07!63;UBERON:0001015!7.80e-07!63;UBERON:0000383!7.80e-07!63
|ontology_enrichment_uberon=UBERON:0002100!6.83e-08!199;UBERON:0004458!1.07e-07!49;UBERON:0002323!3.53e-07!46;UBERON:0004638!9.09e-07!18;UBERON:0001986!9.09e-07!18;UBERON:0004852!9.09e-07!18
|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00139074005097384!CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249821880748681!CTCFL#140690;3:11.8478846153846:0.00120177034853823:0.00815116855636993!ETS1#2113;4:7.78300873776187:0.000512103594768887:0.00444068310644867!HDAC2#3066;4:10.732496189301:0.000145096579747875:0.00188596660762766!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00674395853636833!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318944265526031!RXRA#6256;3:12.04477028348:0.00114526216283683:0.00783608720024345!SMARCC1#6599;3:26.1980155917789:0.000115962562606041:0.00157654439937676!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146388238850495!STAT1#6772;4:16.5652699977594:2.61308619905866e-05:0.000563743254582704!SUZ12#23512;4:40.0926247288503:7.78750287036555e-07:3.41157303807931e-05!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135388500915117!TAF7#6879;3:6.85984164295435:0.00584328640701904:0.0262480425403295!TCF12#6938;3:6.38067894131185:0.00718516865325884:0.0298327037042896
|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00139074005097384!CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249821880748681!CTCFL#140690;3:11.8478846153846:0.00120177034853823:0.00815116855636993!ETS1#2113;4:7.78300873776187:0.000512103594768887:0.00444068310644867!HDAC2#3066;4:10.732496189301:0.000145096579747875:0.00188596660762766!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00674395853636833!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318944265526031!RXRA#6256;3:12.04477028348:0.00114526216283683:0.00783608720024345!SMARCC1#6599;3:26.1980155917789:0.000115962562606041:0.00157654439937676!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146388238850495!STAT1#6772;4:16.5652699977594:2.61308619905866e-05:0.000563743254582704!SUZ12#23512;4:40.0926247288503:7.78750287036555e-07:3.41157303807931e-05!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135388500915117!TAF7#6879;3:6.85984164295435:0.00584328640701904:0.0262480425403295!TCF12#6938;3:6.38067894131185:0.00718516865325884:0.0298327037042896
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}}
}}

Revision as of 11:43, 19 October 2012


Full id: C1813_somatostatinoma_melanoma_mesenchymal_placenta_smallcell_Keratocytes_renal



Phase1 CAGE Peaks

Hg19::chr19:18496957..18496977,+p1@GDF15
Hg19::chr19:18499119..18499128,+p9@GDF15
Hg19::chr19:18499150..18499175,+p3@GDF15
Hg19::chr19:18499210..18499232,+p4@GDF15
Hg19::chr19:18499287..18499309,+p2@GDF15


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
trunk6.83e-08199
body cavity or lining1.07e-0749
body cavity3.53e-0746
blood vessel endothelium9.09e-0718
endothelium9.09e-0718
cardiovascular system endothelium9.09e-0718


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90556.336201576962639.78880505817628e-050.00139074005097384
CTCF#1066455.360256373075030.0002259278299937090.00249821880748681
CTCFL#140690311.84788461538460.001201770348538230.00815116855636993
ETS1#211347.783008737761870.0005121035947688870.00444068310644867
HDAC2#3066410.7324961893010.0001450965797478750.00188596660762766
HEY1#2346254.040111043105710.0009288852205177990.00674395853636833
RAD21#588536.21302033727380.007751055068811640.0318944265526031
RXRA#6256312.044770283480.001145262162836830.00783608720024345
SMARCC1#6599326.19801559177890.0001159625626060410.00157654439937676
SMC3#912639.02695970695970.002650964449467550.0146388238850495
STAT1#6772416.56526999775942.61308619905866e-050.000563743254582704
SUZ12#23512440.09262472885037.78750287036555e-073.41157303807931e-05
TAF1#687253.343046285745290.002394600090870310.0135388500915117
TAF7#687936.859841642954350.005843286407019040.0262480425403295
TCF12#693836.380678941311850.007185168653258840.0298327037042896



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.